Since people have been generally helpful in this thread -- was hoping to get an answer to this question, I've done a bit of research and haven't been able to find a definitive answer:
Is there any difference between the legit CIA installed by FBI and the redownloaded version from the eShop? Is the eShop version "more legit", or does it write to a different directory on the SD card or something?
Also, could I hypothetically do the following if I wanted to?
Install MH4U legit CIA using this tool, launch the game, launch eShop, quit eShop and delete the game using System Settings, then redownload a fresh copy from eShop
Thanks in advance! You all have been awesome and helpful